[BioC] Does illuminaHumanv3BeadID.db correspond to the Illumina HT-12 chip

[Mark Dunning]

Hi,

Thanks for the report. Along with the control probes, we also discard
anything that is poorly annotated on the array (see our website:-
http://www.compbio.group.cam.ac.uk/Resources/Annotation/index.html)

However, on this occasion I think there are more probes missing than I
would expect. I'll have to check the input to the annotation packages
and re-build if necessary.

Regards,

Mark

On Wed, Nov 11, 2009 at 5:07 AM, Macartney, Donia
<Donia.Macartney at esr.cri.nz> wrote:
> Dear Matt
>
> Thanks for replying quickly.
>
> I don't think (hope) I haven't done anything dumb....
>
> but
>
> I checked controls against my toptable and they didn't overlap. So I definitely have some non-control probes that are missing from the annotation package.
>
> I've also looked at the number of probes in my array data and I have 48,803, and this matches the number in the HT-12 annotation file from Illumina (I'll send you a copy). So I guess the information used to create the annotation file was different.
>
> How do I go about creating my own annotation package?
>
> Many thanks for you help
>
> Best wishes
>
> Donia
>
>
>
> -----Original Message-----
> From: Matthew Ritchie [mailto:mritchie at wehi.EDU.AU]
> Sent: Wednesday, 11 November 2009 1:57 p.m.
> To: Macartney, Donia
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Does illuminaHumanv3BeadID.db correspond to the Illumina HT-12 chip
>
> Dear Donia,
>
>> Sorry if I've missed this somewhere
>>
>> I'm analysing new data from an Human Illumina HT-12 v3 BeadChip. I'm
>> using BeadID as the identifier however the  illuminaHumanv3BeadID.db
>> package seems to be missing some of the Bead Ids from my top table
>> list. Is there a different package I can use - or what packages should
>> I use to create my own annotation package?
>
> You are using the correct package.  Note that this annotation package (and most others available from BioC) only contains information for non-control probes.  Maybe the probes in question are controls?  You can get a list of control BeadIDs for Human v3 chips using the following commands - check to see whether any of these match up with the ones in your top table.
>
> library(beadarray)
> data(ExpressionControlData)
> ExpressionControlData$Humanv3[,1]
>
> I hope this helps.  Best wishes,
>
> Matt
>
>
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